Natural selection on synonymous genetic variation in the major histocompatibility complex

Protein coding DNA sequences harbor synonymous nucleotide variation that does not change amino acid sequences but influences phenotypes via multiple effects on the pathway from gene to protein. Synonymous variation has recently been shown to coevolve between viruses and their natural hosts, but its potential role in host immune defenses has not been explored. Here, I present evidence of natural selection on synonymous variation in the major histocompatibility complex (MHC), a highly polymorphic multigene locus that plays a crucial role in pathogen recognition by the adaptive immune system of vertebrate species. Using data from a wild population of Great Reed Warblers, I show that codon usage in exon 3 of MHC class I (MHC-I) genes is under strong purifying selection in 56 out of 87 codon sites. Scanning the Great Reed Warbler genome for tRNA genes revealed that, for most amino acids, bias towards preferred codons was associated with abundances of tRNA isotypes, indicating that the purifying selection is likely driven by selection for increased translational efficiency. However, spikes of synonymous variation appeared in 31 of the 87 sites in the MHC-I exon 3, and in those sites, codon usage bias and correlations with tRNA abundances were reduced. The distribution of the spikes of synonymous variation showed no consistent association with structural domains of the MHC-I protein, nor with sites under positive selection for amino acid change, which are considered important for antigen binding properties. Intriguingly, the amount of synonymous variation in genotypes showed a positive correlation with Darwinian fitness, indicating that important evolutionary forces are at play that neutralize purifying selection in the 31 sites. From an ultimate perspective, the release of purifying selection among certain sites in MHC genes may indicate an arms race with pathogens, and I propose that the spikes of synonymous variation may reveal a footprint of natural selection on MHC genes to escape inhibitory molecular interactions between intracellular pathogens and MHC mRNA. Unravelling the mechanisms of such interactions should be of great importance to our understanding of this extremely important locus and I hope that the results and methodological advancements presented here will spark future studies of synonymous variation in the MHC and its biological effects.